scholarly journals Genome-Wide Screen in Francisella novicida for Genes Required for Pulmonary and Systemic Infection in Mice

2008 ◽  
Vol 77 (1) ◽  
pp. 232-244 ◽  
Author(s):  
Petra S. Kraemer ◽  
Allison Mitchell ◽  
Mark R. Pelletier ◽  
Larry A. Gallagher ◽  
Mike Wasnick ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Systemic Infection ◽  
Single Strain ◽  
Francisella Novicida ◽  
Transposon Insertion ◽  
Genome Wide ◽  
Significant Enrichment ◽  
Life Threatening ◽  
Transposon Mutants ◽  
Insertion Mutants

ABSTRACT Francisella tularensis is a gram-negative, highly infectious, aerosolizable facultative intracellular pathogen that causes the potentially life-threatening disease tularemia. To date there is no approved vaccine available, and little is known about the molecular mechanisms important for infection, survival, and dissemination at different times of infection. We report the first whole-genome screen using an inhalation mouse model to monitor infection in the lung and dissemination to the liver and spleen. We queried a comprehensive library of 2,998 sequence-defined transposon insertion mutants in Francisella novicida strain U112 using a microarray-based negative-selection screen. We were able to track the behavior of 1,029 annotated genes, equivalent to a detection rate of 75% and corresponding to ∼57% of the entire F. novicida genome. As expected, most transposon mutants retained the ability to colonize, but 125 candidate virulence genes (12%) could not be detected in at least one of the three organs. They fell into a variety of functional categories, with one-third having no annotated function and a statistically significant enrichment of genes involved in transcription. Based on the observation that behavior during complex pool infections correlated with the degree of attenuation during single-strain infection we identified nine genes expected to strongly contribute to infection. These included two genes, those for ATP synthase C (FTN_1645) and thioredoxin (FTN_1415), that when mutated allowed increased host survival and conferred protection in vaccination experiments.

scholarly journals Genome-Wide Identification of Francisella tularensis Virulence Determinants

2007 ◽  
Vol 75 (6) ◽  
pp. 3089-3101 ◽  
Author(s):  
Jingliang Su ◽  
Jun Yang ◽  
Daimin Zhao ◽  
Thomas H. Kawula ◽  
Jeffrey A. Banas ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Stress Responses ◽  
Small Subset ◽  
Virulence Determinants ◽  
Genome Wide ◽  
Genes Encoding ◽  
Capsule Locus ◽  
Life Threatening ◽  
Transposon Mutants ◽  
Schu S4

ABSTRACT Francisella tularensis is a gram-negative pathogen that causes life-threatening infections in humans and has potential for use as a biological weapon. The genetic basis of the F. tularensis virulence is poorly understood. This study screened a total of 3,936 transposon mutants of the live vaccine strain for infection in a mouse model of respiratory tularemia by signature-tagged mutagenesis. We identified 341 mutants attenuated for infection in the lungs. The transposon disruptions were mapped to 95 different genes, virtually all of which are also present in the genomes of other F. tularensis strains, including human pathogenic F. tularensis strain Schu S4. A small subset of these attenuated mutants carried insertions in the genes encoding previously known virulence factors, but the majority of the identified genes have not been previously linked to F. tularensis virulence. Among these are genes encoding putative membrane proteins, proteins associated with stress responses, metabolic proteins, transporter proteins, and proteins with unknown functions. Several attenuated mutants contained disruptions in a putative capsule locus which partially resembles the poly-γ-glutamate capsule biosynthesis locus of Bacillus anthracis, the anthrax agent. Deletional mutation analysis confirmed that this locus is essential for F. tularensis virulence.

scholarly journals Identification of genes that contribute to fitness of African and Global clades of Salmonella Enteritidis during infection of macrophages

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Wai Yee Fong ◽  
Rocío Canals ◽  
Alex Predeus ◽  
Blanca Perez-Sepulveda ◽  
Nicholas A. Feasey
Keyword(s):  
Salmonella Enteritidis ◽  
Systemic Infection ◽  
Bloodstream Infections ◽  
Host Cells ◽  
Bacterial Survival ◽  
Global Epidemic ◽  
Global Regulators ◽  
Transposon Insertion ◽  
Transposon Insertion Sequencing ◽  
Insertion Mutants

Non-typhoidal Salmonella (NTS) usually cause gastroenteritis in humans, but in recent years NTS have begun to cause epidemics of bloodstream infections in Africa. Salmonella Enteritidis is the second most common serovar associated with this invasive form of NTS disease (iNTS) in Africa. To establish a systemic infection, Salmonella must survive and replicate within host cells, with macrophages being a primary target. Genomic characterisation of S. Enteritidis isolates from human bloodstream has identified two new clades that are unique to Africa and distinct from the Global Epidemic clade. The African S. Enteritidis clades exhibit genomic degradation, and possess a distinct prophage repertoire and are multi-drug resistant. However, little is known about the virulence factors that allow African S. Enteritidis to cause systemic infection in susceptible hosts. We screened libraries of random insertion mutants of African and Global S. Enteritidis by transposon insertion sequencing (TIS), and identified about 280 genes belonging to each clade that contribute to bacterial survival and replication in murine macrophages. The genes were associated with 5 pathogenicity-islands, or encoded the global regulators PhoPQ and OmpR-EnvZ. Experiments are ongoing to investigate the role in intra-macrophage replication of genes that are uniquely identified in African Salmonella. It is hoped that our findings will contribute to a greater understanding of African Salmonella infection biology, and that some of the virulence-associated genes could be potential targets for novel therapeutics.

scholarly journals A Genome-Wide Collection of Mos1 Transposon Insertion Mutants for the C. elegans Research Community

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e30482 ◽  
Author(s):  
Elodie Vallin ◽  
Joseph Gallagher ◽  
Laure Granger ◽  
Edwige Martin ◽  
Jérôme Belougne ◽  
...  
Keyword(s):  
Research Community ◽  
C Elegans ◽  
Transposon Insertion ◽  
Genome Wide ◽  
A Genome ◽  
Insertion Mutants

scholarly journals Chloromethane Metabolism byMethylobacterium sp. Strain CM4

1998 ◽  
Vol 64 (5) ◽  
pp. 1933-1936 ◽  
Author(s):  
Todd Vannelli ◽  
Alex Studer ◽  
Michael Kertesz ◽  
Thomas Leisinger
Keyword(s):  
Growth Characteristics ◽  
Protein Yield ◽  
Cell Protein ◽  
Yield Data ◽  
Whole Cell ◽  
Molar Yield ◽  
Transposon Insertion ◽  
Transposon Mutants ◽  
Whole Cell Protein ◽  
Insertion Mutants

ABSTRACT Methylobacterium sp. strain CM4 metabolized chloromethane quantitatively with a molar yield of 2.8 g of whole-cell protein/mol of C. This value was similar to that observed after growth with methanol (2.9 g of protein/mol of C) and about three times larger than the yield with formate (0.94 g of protein/mol of C). Chloromethane dehalogenation activity was inducible. MiniTn5 transposon insertion mutants with altered growth characteristics with chloromethane and other C1 compounds were isolated and characterized. Nine of these were unable to grow with chloromethane but were able to grow with methanol, methylamine, or formate. Seventy-three transposon mutants that were defective in the utilization of either methanol, methylamine, methanol plus methylamine, or formate could still grow with chloromethane. Based on the protein yield data and the properties of the transposon mutants, we propose a pathway for chloromethane metabolism that depends on methyltransferase and dehydrogenase activities.

scholarly journals Isolation and Characterization of Xenorhabdus nematophila Transposon Insertion Mutants Defective in Lipase Activity against Tween

2009 ◽  
Vol 191 (16) ◽  
pp. 5325-5331 ◽  
Author(s):  
Gregory R. Richards ◽  
Eugenio I. Vivas ◽  
Aaron W. Andersen ◽  
Delmarie Rivera-Santos ◽  
Sara Gilmore ◽  
...  
Keyword(s):  
Lipase Activity ◽  
Metabolic Pathways ◽  
Lipase Production ◽  
Xenorhabdus Nematophila ◽  
Transposon Insertion ◽  
Isolation And Characterization ◽  
Transposon Mutants ◽  
Conserved Gene ◽  
Insertion Mutants

ABSTRACT We identified Xenorhabdus nematophila transposon mutants with defects in lipase activity. One of the mutations, in yigL, a conserved gene of unknown function, resulted in attenuated virulence against Manduca sexta insects. We discuss possible connections between lipase production, YigL, and specific metabolic pathways.

scholarly journals Attenuated Francisella novicida Transposon Mutants Protect Mice against Wild-Type Challenge

2006 ◽  
Vol 74 (9) ◽  
pp. 5095-5105 ◽  
Author(s):  
Rebecca Tempel ◽  
Xin-He Lai ◽  
Lidia Crosa ◽  
Briana Kozlowicz ◽  
Fred Heffron
Keyword(s):  
Bacterial Pathogen ◽  
Host Cells ◽  
Wild Type ◽  
Live Attenuated Vaccine ◽  
Francisella Novicida ◽  
Mouse Macrophages ◽  
Life Threatening ◽  
Transposon Mutants ◽  
High Doses ◽  
Schu S4

ABSTRACT Francisella tularensis is the bacterial pathogen that causes tularemia in humans and a number of animals. To date, there is no approved vaccine for this widespread and life-threatening disease. The goal of this study was to identify F. tularensis mutants that can be used in the development of a live attenuated vaccine. We screened F. novicida transposon mutants to identify mutants that exhibited reduced growth in mouse macrophages, as these cells are the preferred host cells of Francisella and an essential component of the innate immune system. This approach yielded 16 F. novicida mutants that were 100-fold more attenuated for virulence in a mouse model than the wild-type parental strain. These mutants were then tested to determine their abilities to protect mice against challenge with high doses of wild-type bacteria. Five of the 16 attenuated mutants (with mutations corresponding to dsbB, FTT0742, pdpB, fumA, and carB in the F. tularensis SCHU S4 strain) provided mice with protection against challenge with high doses (>8 × 105 CFU) of wild-type F. novicida. We believe that these findings will be of use in the design of a vaccine against tularemia.

scholarly journals Establishment of a Functional Genomics Platform for Leifsonia xyli subsp. xyli

2004 ◽  
Vol 17 (2) ◽  
pp. 175-183 ◽  
Author(s):  
Stevens M. Brumbley ◽  
Lars A. Petrasovits ◽  
Rachel M. Murphy ◽  
Roland J. Nagel ◽  
Judith M. Candy ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Integral Membrane Protein ◽  
Open Reading Frames ◽  
Nucleotide Sequencing ◽  
Transposon Insertion ◽  
Rapid Polymerase Chain Reaction ◽  
Before And After ◽  
Transposon Mutants ◽  
Flanking Regions ◽  
Slow Growing

Leifsonia xyli subsp. xyli, the causal agent of ratoon stunting disease in sugarcane, is a xylem-limited, nutritionally fastidious, slow growing, gram-positive coryneform bacterium. Because of the difficulties in growing this bacterium in pure culture, little is known about the molecular mechanisms of pathogenesis. Currently, the genome sequence of L. xyli subsp. xyli is being completed by the Agronomical and Environmental Genomes group from the Organization for Nucleotide Sequencing and Analysis in Brazil. To complement this work, we produced 712 Lxx∷Tn4431 transposon mutants and sequenced flanking regions from 383 of these, using a rapid polymerase chain reaction-based approach. Tn4431 insertions appeared to be widespread throughout the L. xyli subsp. xyli genome; however, there were regions that had significantly higher concentrations of insertions. The Tn4431 mutant library was screened for individuals unable to colonize sugarcane, and one noncolonizing mutant was found. The mutant contained a transposon insertion disrupting two open reading frames (ORF), one of which had homology to an integral membrane protein from Mycobacterium leprae. Sequencing of the surrounding regions revealed two operons, pro and cyd, both of which are believed to play roles in disease. Complementation studies were carried out using the noncolonizing Lxx∷Tn4431 mutant. The noncolonizing mutant was transformed with a cosmid containing 40 kbp of wild-type sequence, which included the two ORF disrupted in the mutant, and several transformants were subsequently able to colonize sugarcane. However, analysis of each of these transformants, before and after colonization, suggests that they have all undergone various recombinant events, obscuring the roles of these ORF in L. xyli subsp. xyli pathogenesis.

Artificial Intelligence for epigenetics: towards personalized medicine

2020 ◽  
Vol 27 ◽  
Author(s):  
Giulia De Riso ◽  
Sergio Cocozza
Keyword(s):  
Biological Sciences ◽  
Artificial Intelligence ◽  
Personalized Medicine ◽  
Molecular Mechanisms ◽  
Genomic Sequence ◽  
Health Care Interventions ◽  
Genome Wide ◽  
Genetic And Environmental Factors ◽  
Opening Up ◽  
Omic Data

: Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mechanisms, that is in turn orchestrated by genetic and environmental factors. The epigenetic profile captures the unique regulatory landscape and the exposure to environmental stimuli of an individual. It thus constitutes a valuable reservoir of information for personalized medicine, which is aimed at customizing health-care interventions based on the unique characteristics of each individual. Nowadays, the complex milieu of epigenomic marks can be studied at the genome-wide level thanks to massive, highthroughput technologies. This new experimental approach is opening up new and interesting knowledge perspectives. However, the analysis of these complex omic data requires to face important analytic issues. Artificial Intelligence, and in particular Machine Learning, are emerging as powerful resources to decipher epigenomic data. In this review, we will first describe the most used ML approaches in epigenomics. We then will recapitulate some of the recent applications of ML to epigenomic analysis. Finally, we will provide some examples of how the ML approach to epigenetic data can be useful for personalized medicine.

scholarly journals Impairing flow-mediated endothelial remodeling reduces extravasation of tumor cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gautier Follain ◽  
Naël Osmani ◽  
Valentin Gensbittel ◽  
Nandini Asokan ◽  
Annabel Larnicol ◽  
...  
Keyword(s):  
Blood Flow ◽  
Tumor Cells ◽  
Molecular Mechanisms ◽  
Metastatic Progression ◽  
Metastatic Dissemination ◽  
Secondary Tumors ◽  
Flow Profiles ◽  
Endothelial Response ◽  
Life Threatening

AbstractTumor progression and metastatic dissemination are driven by cell-intrinsic and biomechanical cues that favor the growth of life-threatening secondary tumors. We recently identified pro-metastatic vascular regions with blood flow profiles that are permissive for the arrest of circulating tumor cells. We have further established that such flow profiles also control endothelial remodeling, which favors extravasation of arrested CTCs. Yet, how shear forces control endothelial remodeling is unknown. In the present work, we aimed at dissecting the cellular and molecular mechanisms driving blood flow-dependent endothelial remodeling. Transcriptomic analysis of endothelial cells revealed that blood flow enhanced VEGFR signaling, among others. Using a combination of in vitro microfluidics and intravital imaging in zebrafish embryos, we now demonstrate that the early flow-driven endothelial response can be prevented upon specific inhibition of VEGFR tyrosine kinase and subsequent signaling. Inhibitory targeting of VEGFRs reduced endothelial remodeling and subsequent metastatic extravasation. These results confirm the importance of VEGFR-dependent endothelial remodeling as a driving force of CTC extravasation and metastatic dissemination. Furthermore, the present work suggests that therapies targeting endothelial remodeling might be a relevant clinical strategy in order to impede metastatic progression.

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